PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
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Fatal error pigeon classify . Problem with cage-peak bed file #656

Closed davidvilanova closed 1 month ago

davidvilanova commented 5 months ago

Hi, i have gone through the isoseq pipeline (using latest isoseq version).

isoseq 4.0.0 (commit v4.0.0)

Using:
  pbbam     : 2.4.99 (commit v2.4.0-16-g5cc6e4b)
  pbcopper  : 2.3.99 (commit v2.3.0-14-g5ac5693)
  pbmm2     : 1.11.99 (commit v1.11.0-1-g1b5a417)
  minimap2  : 2.15
  parasail  : 2.1.3
  boost     : 1.77
  htslib    : 1.17
  zlib      : 1.2.13

pigeon 1.2.0 (commit -v1.2.0)

Using:
  pbbam     : 2.5.0 (commit v2.5.0)
  pbcopper  : 2.4.0 (commit v2.4.0)
  boost     : 1.76
  htslib    : 1.17
  zlib      : 1.2.11

When classifying the transcripts using pigeon classify i get this error:

pigeon classify -j ${CPUS} --fl ${collapse}/${part}.isoform.flnc_count.txt --log-file ${classification}/${part}.log --cage-peak ${tss} --out-dir ${classification} ${collapse}/${part}.isoform.sorted.gff ${gtf} ${genomefa}

| 20240229 09:22:59.986 | WARN | Skipping reference (MU273394.1) - missing from CAGE peak data
| 20240229 09:22:59.986 | WARN | Skipping reference (MU273395.1) - missing from reference annotations
| 20240229 09:22:59.986 | WARN | Skipping reference (MU273395.1) - missing from CAGE peak data
| 20240229 09:22:59.986 | WARN | Skipping reference (MU273397.1) - missing from reference annotations
| 20240229 09:22:59.986 | WARN | Skipping reference (MU273397.1) - missing from CAGE peak data
| 20240229 09:23:22.665 | FATAL | pigeon classify ERROR: invalid BED line: 66   rfhg_2.1        1       -

This the header of my cage-peak bed file:

bed file: refTSS_v4.1_human_coordinate.hg38.bed [](coming from https://reftss.riken.jp/datafiles/current/human/)

chr1    16013   16020   rfhg_1.1        1       -
chr1    29346   29366   rfhg_2.1        1       -
chr1    36521   36538   rfhg_3.1        1       +
armintoepfer commented 1 month ago

Please let us know if you still have this error. Closing until then. Looks like an issue with your bed.